Add function to check data to avoid incorrect allele encoding

python/tests/beagle_numba.py

@@ -87,6 +87,30 @@ def remap_alleles(a):
     return b
 
 
+def check_data(ref_h, query_h):
+    """
+    For each site, check if the alleles in the query haplotype
+    are represented in the reference haplotypes.
+
+    Missing data (i.e. -1) are ignored.
+
+    :param numpy.ndarray ref_h: Reference haplotypes.
+    :param numpy.ndarray query_h: One query haplotype.
+    :return: True if alleles in query are in reference.
+    :rtype: bool
+    """
+    m = ref_h.shape[0]
+    assert m == len(query_h), "Reference and query differ in length."
+    for i in range(m):
+        if query_h[i] == -1:
+            continue
+        else:
+            if query_h[i] not in ref_h[i, :]:
+                print(f"Allele {query_h[i]} at {i}th position not in reference.")
+                return False
+    return True
+
+
 def convert_to_genetic_map_positions(pos, genetic_map=None):
     """
     Convert physical positions (bp) to genetic map positions (cM).